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Aliases for VLDLR Gene

Aliases for VLDLR Gene

  • Very Low Density Lipoprotein Receptor 2 3 5
  • VLDL Receptor 3 4
  • VLDL-R 3 4
  • Very Low-Density Lipoprotein Receptor 3
  • VLDLRCH 3
  • CAMRQ1 3
  • CARMQ1 3
  • CHRMQ1 3

External Ids for VLDLR Gene

Previous GeneCards Identifiers for VLDLR Gene

  • GC09P002776
  • GC09P002603
  • GC09P002612

Summaries for VLDLR Gene

Entrez Gene Summary for VLDLR Gene

  • The low density lipoprotein receptor (LDLR) gene family consists of cell surface proteins involved in receptor-mediated endocytosis of specific ligands. This gene encodes a lipoprotein receptor that is a member of the LDLR family and plays important roles in VLDL-triglyceride metabolism and the reelin signaling pathway. Mutations in this gene cause VLDLR-associated cerebellar hypoplasia. Alternative splicing generates multiple transcript variants encoding distinct isoforms for this gene. [provided by RefSeq, Aug 2009]

GeneCards Summary for VLDLR Gene

VLDLR (Very Low Density Lipoprotein Receptor) is a Protein Coding gene. Diseases associated with VLDLR include Cerebellar Hypoplasia And Mental Retardation With Or Without Quadrupedal Locomotion 1 and Femoral Neuropathy. Among its related pathways are Lipoprotein metabolism and Lissencephaly gene (LIS1) in neuronal migration and development. GO annotations related to this gene include calcium ion binding and glycoprotein binding. An important paralog of this gene is LRP8.

UniProtKB/Swiss-Prot for VLDLR Gene

  • Binds VLDL and transports it into cells by endocytosis. In order to be internalized, the receptor-ligand complexes must first cluster into clathrin-coated pits. Binding to Reelin induces tyrosine phosphorylation of Dab1 and modulation of Tau phosphorylation (By similarity).

Gene Wiki entry for VLDLR Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for VLDLR Gene

Genomics for VLDLR Gene

Regulatory Elements for VLDLR Gene

Enhancers for VLDLR Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH09G002418 0.7 ENCODE 42.5 -202.8 -202784 1.5 MAZ ZNF384 FEZF1 ZIC2 ATF2 OSR2 PRDM6 SMARCA4 BCL6B PRDM10 VLDLR LOC105375956 LOC101930053
GH09G002411 0.7 ENCODE 37.2 -208.8 -208809 3.6 PKNOX1 TEAD4 MAX DPF2 FOXA1 RAD51 JUND CTBP1 GATA3 FOS VLDLR LOC105375956 LOC101930053
GH09G002728 1.2 Ensembl ENCODE 10.9 +106.4 106429 0.6 FOXA2 PKNOX1 WRNIP1 ZNF2 YY1 TCF12 CBX5 ZNF143 REST TSHZ1 VLDLR-AS1 VLDLR GC09M002715 PIR50784
GH09G002559 0.9 Ensembl ENCODE 12 -61.7 -61709 1.8 FOXA2 RFX1 BHLHE40 USF2 SIN3A MAX RAD21 NR2F2 JUND VLDLR ENSG00000231052 GC09P002596
GH09G002620 1 ENCODE 10.2 +1.2 1223 4.1 WRNIP1 SIN3A DMAP1 ZNF2 ZNF48 SP3 NFYC MXD4 REST KAT8 VLDLR PIR48978
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around VLDLR on UCSC Golden Path with GeneCards custom track

Promoters for VLDLR Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000232545 521 2001 WRNIP1 SIN3A DMAP1 ZNF2 ZNF48 FOS SP3 NFYC REST KAT8

Genomic Location for VLDLR Gene

Chromosome:
9
Start:
2,621,679 bp from pter
End:
2,660,053 bp from pter
Size:
38,375 bases
Orientation:
Plus strand

Genomic View for VLDLR Gene

Genes around VLDLR on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
VLDLR Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for VLDLR Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for VLDLR Gene

Proteins for VLDLR Gene

  • Protein details for VLDLR Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P98155-VLDLR_HUMAN
    Recommended name:
    Very low-density lipoprotein receptor
    Protein Accession:
    P98155
    Secondary Accessions:
    • B2RMZ7
    • D3DRH6
    • Q5VVF6

    Protein attributes for VLDLR Gene

    Size:
    873 amino acids
    Molecular mass:
    96098 Da
    Quaternary structure:
    • Binds to the extracellular matrix protein Reelin. Interacts with VLDLR. Interacts with SNX17 (By similarity). Interacts with DAB1. Receptor for the minor-group human rhinoviruses (HRVs); binds protein VP1 through the second and third LDL-receptor class A domains. Interacts with PCSK9.

    Three dimensional structures from OCA and Proteopedia for VLDLR Gene

    Alternative splice isoforms for VLDLR Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for VLDLR Gene

Post-translational modifications for VLDLR Gene

  • Ubiquitinated at Lys-839 by MYLIP leading to degradation.
  • Ubiquitination at Lys828 and Lys839
  • Glycosylation at Thr71, posLast=151151, Thr277, posLast=765765, and Asn781
  • Modification sites at PhosphoSitePlus

Other Protein References for VLDLR Gene

Antibody Products

  • Cloud-Clone Corp. Antibodies for VLDLR

Protein Products

  • Novus Biologicals lysates for VLDLR

No data available for DME Specific Peptides for VLDLR Gene

Domains & Families for VLDLR Gene

Gene Families for VLDLR Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with VLDLR: view

No data available for UniProtKB/Swiss-Prot for VLDLR Gene

Function for VLDLR Gene

Molecular function for VLDLR Gene

GENATLAS Biochemistry:
very low density lipoprotein/ApoE receptor,containing a CGG repeat in 5utr,(may be a susceptibility gene for late onset senile Alzheimer disease)
UniProtKB/Swiss-Prot Function:
Binds VLDL and transports it into cells by endocytosis. In order to be internalized, the receptor-ligand complexes must first cluster into clathrin-coated pits. Binding to Reelin induces tyrosine phosphorylation of Dab1 and modulation of Tau phosphorylation (By similarity).

Gene Ontology (GO) - Molecular Function for VLDLR Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001948 glycoprotein binding IPI 10571240
GO:0005041 low-density lipoprotein receptor activity TAS 10380922
GO:0005509 calcium ion binding IEA --
GO:0005515 protein binding IPI 8083232
GO:0030229 very-low-density lipoprotein particle receptor activity IDA 8083232
genes like me logo Genes that share ontologies with VLDLR: view
genes like me logo Genes that share phenotypes with VLDLR: view

Human Phenotype Ontology for VLDLR Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for VLDLR Gene

MGI Knock Outs for VLDLR:

Animal Model Products

  • Taconic Biosciences Mouse Models for VLDLR

CRISPR Products

miRNA for VLDLR Gene

miRTarBase miRNAs that target VLDLR

Inhibitory RNA Products

Clone Products

Cell Line Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for VLDLR Gene

Localization for VLDLR Gene

Subcellular locations from UniProtKB/Swiss-Prot for VLDLR Gene

Membrane; Single-pass type I membrane protein. Membrane, clathrin-coated pit; Single-pass type I membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for VLDLR gene
Compartment Confidence
plasma membrane 5
lysosome 5
extracellular 4
cytoskeleton 2
peroxisome 2
mitochondrion 1
endoplasmic reticulum 1
endosome 1

Gene Ontology (GO) - Cellular Components for VLDLR Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005615 extracellular space IEA --
GO:0005765 lysosomal membrane TAS --
GO:0005886 plasma membrane TAS --
GO:0005905 clathrin-coated pit IEA --
GO:0016020 membrane IDA 15082773
genes like me logo Genes that share ontologies with VLDLR: view

Pathways & Interactions for VLDLR Gene

genes like me logo Genes that share pathways with VLDLR: view

SIGNOR curated interactions for VLDLR Gene

Is activated by:

Gene Ontology (GO) - Biological Process for VLDLR Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription from RNA polymerase II promoter ISS --
GO:0006629 lipid metabolic process IEA --
GO:0006810 transport IEA --
GO:0006869 lipid transport IEA --
GO:0006897 endocytosis IEA --
genes like me logo Genes that share ontologies with VLDLR: view

Drugs & Compounds for VLDLR Gene

(5) Drugs for VLDLR Gene - From: DrugBank and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
lauric acid Experimental Pharma Agonist, Target 0

(7) Additional Compounds for VLDLR Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with VLDLR: view

Transcripts for VLDLR Gene

Unigene Clusters for VLDLR Gene

Very low density lipoprotein receptor:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for VLDLR Gene

ExUns: 1 ^ 2a · 2b ^ 3a · 3b ^ 4 ^ 5a · 5b ^ 6 ^ 7a · 7b ^ 8a · 8b ^ 9a · 9b ^ 10a · 10b ^ 11 ^ 12 ^ 13 ^ 14a · 14b ^ 15a · 15b ^ 16a · 16b ·
SP1: - - -
SP2: -
SP3:
SP4: -
SP5: -
SP6: -
SP7:
SP8:
SP9:

ExUns: 16c
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:

Relevant External Links for VLDLR Gene

GeneLoc Exon Structure for
VLDLR
ECgene alternative splicing isoforms for
VLDLR

Expression for VLDLR Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for VLDLR Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for VLDLR Gene

This gene is overexpressed in Ovary (x5.6) and Heart - Left Ventricle (x5.4).

Protein differential expression in normal tissues from HIPED for VLDLR Gene

This gene is overexpressed in Adrenal (33.2) and Testis (15.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for VLDLR Gene



Protein tissue co-expression partners for VLDLR Gene

NURSA nuclear receptor signaling pathways regulating expression of VLDLR Gene:

VLDLR

SOURCE GeneReport for Unigene cluster for VLDLR Gene:

Hs.370422

mRNA Expression by UniProt/SwissProt for VLDLR Gene:

P98155-VLDLR_HUMAN
Tissue specificity: Abundant in heart and skeletal muscle; also ovary and kidney; not in liver.

Evidence on tissue expression from TISSUES for VLDLR Gene

  • Heart(4.6)
  • Muscle(4.5)
  • Nervous system(4.2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for VLDLR Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • integumentary
  • nervous
  • respiratory
  • skeletal muscle
  • skeleton
Organs:
Head and neck:
  • brain
  • cerebellum
  • cranial nerve
  • eye
  • face
  • head
  • jaw
  • lip
  • mandible
  • maxilla
  • mouth
  • neck
  • skull
Thorax:
  • lung
  • rib
  • rib cage
Pelvis:
  • pelvis
Limb:
  • foot
  • hand
  • lower limb
  • upper limb
General:
  • hair
  • peripheral nerve
  • peripheral nervous system
  • skin
  • spinal column
  • spinal cord
  • vertebrae
genes like me logo Genes that share expression patterns with VLDLR: view

Primer Products

Orthologs for VLDLR Gene

This gene was present in the common ancestor of animals.

Orthologs for VLDLR Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia VLDLR 34 35
  • 99.62 (n)
dog
(Canis familiaris)
Mammalia VLDLR 34 35
  • 91.56 (n)
cow
(Bos Taurus)
Mammalia VLDLR 34 35
  • 91.16 (n)
rat
(Rattus norvegicus)
Mammalia Vldlr 34
  • 91.07 (n)
mouse
(Mus musculus)
Mammalia Vldlr 34 16 35
  • 90.95 (n)
oppossum
(Monodelphis domestica)
Mammalia VLDLR 35
  • 90 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia VLDLR 35
  • 71 (a)
OneToOne
chicken
(Gallus gallus)
Aves VLDL 35
  • 80 (a)
OneToOne
VLDLR 34
  • 79.1 (n)
lizard
(Anolis carolinensis)
Reptilia VLDLR 35
  • 71 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia vldlr 34
  • 72.39 (n)
Str.8622 34
African clawed frog
(Xenopus laevis)
Amphibia Xl.998 34
zebrafish
(Danio rerio)
Actinopterygii vldlr 34 35
  • 68.57 (n)
zgc55792 34
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.11520 34
fruit fly
(Drosophila melanogaster)
Insecta LpR1 34 35
  • 51.1 (n)
CG4861 36
  • 40 (a)
LpR2 35
  • 33 (a)
ManyToMany
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP002186 34
  • 50.34 (n)
worm
(Caenorhabditis elegans)
Secernentea T13C2.6 34 35
  • 50.53 (n)
R01H2.3 36
  • 38 (a)
B0244.8 36
  • 37 (a)
Species where no ortholog for VLDLR was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for VLDLR Gene

ENSEMBL:
Gene Tree for VLDLR (if available)
TreeFam:
Gene Tree for VLDLR (if available)

Paralogs for VLDLR Gene

Paralogs for VLDLR Gene

(17) SIMAP similar genes for VLDLR Gene using alignment to 3 proteins:

Pseudogenes.org Pseudogenes for VLDLR Gene

genes like me logo Genes that share paralogs with VLDLR: view

Variants for VLDLR Gene

Sequence variations from dbSNP and Humsavar for VLDLR Gene

SNP ID Clin Chr 09 pos Sequence Context AA Info Type
rs397514750 Pathogenic 2,650,382(+) TTGGT(G/T)TGAAG nc-transcript-variant, reference, missense
rs398122380 Pathogenic 2,645,017(+) AGGCG(-/GTTACAA)GTGTG nc-transcript-variant, reference, frameshift-variant
rs745973997 Pathogenic 2,646,435(+) CTACT(A/G)GACTG nc-transcript-variant, reference, stop-gained
rs770269674 Pathogenic 2,635,452(+) TTCTA(A/G)GGAGA splice-acceptor-variant
rs80338905 Pathogenic 2,645,603(+) CTAAT(A/C/T)GAAGA nc-transcript-variant, reference, synonymous-codon

Structural Variations from Database of Genomic Variants (DGV) for VLDLR Gene

Variant ID Type Subtype PubMed ID
nsv1020530 CNV gain 25217958
nsv1029876 CNV gain 25217958
nsv1133705 CNV deletion 24896259
nsv527298 CNV loss 19592680
nsv613137 CNV gain 21841781
nsv824819 CNV gain 20364138

Variation tolerance for VLDLR Gene

Residual Variation Intolerance Score: 13% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.66; 65.83% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for VLDLR Gene

Human Gene Mutation Database (HGMD)
VLDLR
SNPedia medical, phenotypic, and genealogical associations of SNPs for
VLDLR

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for VLDLR Gene

Disorders for VLDLR Gene

MalaCards: The human disease database

(15) MalaCards diseases for VLDLR Gene - From: OMIM, ClinVar, GeneTests, Orphanet, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
cerebellar hypoplasia and mental retardation with or without quadrupedal locomotion 1
  • vldlr-associated cerebellar hypoplasia
femoral neuropathy
  • femoral nerve dysfunction
cerebellar hypoplasia
  • cerebellar hypoplasia-tapetoretinal degeneration syndrome
lissencephaly with cerebellar hypoplasia
  • lissencephaly 2
cerebellar ataxia, mental retardation and dysequlibrium syndrome
  • camrq
- elite association - COSMIC cancer census association via MalaCards
Search VLDLR in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

VLDLR_HUMAN
  • Cerebellar ataxia, mental retardation, and dysequilibrium syndrome 1 (CAMRQ1) [MIM:224050]: A congenital, non-progressive cerebellar ataxia associated with disturbed equilibrium, delayed ambulation, mental retardation, cerebellar hypoplasia and mild cerebral gyral simplification. Additional features include short stature, strabismus, pes planus and, rarely, seizures. {ECO:0000269 PubMed:16080122}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for VLDLR

Genetic Association Database (GAD)
VLDLR
Human Genome Epidemiology (HuGE) Navigator
VLDLR
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
VLDLR
genes like me logo Genes that share disorders with VLDLR: view

No data available for Genatlas for VLDLR Gene

Publications for VLDLR Gene

  1. The proprotein convertase PCSK9 induces the degradation of low density lipoprotein receptor (LDLR) and its closest family members VLDLR and ApoER2. (PMID: 18039658) Poirier S. … Seidah N.G. (J. Biol. Chem. 2008) 3 4 22 64
  2. A common VLDLR polymorphism interacts with APOE genotype in the prediction of carotid artery disease risk. (PMID: 18056683) Crawford D.C. … Jarvik G.P. (J. Lipid Res. 2008) 3 22 46 64
  3. Functional candidate genes in age-related macular degeneration: significant association with VEGF, VLDLR, and LRP6. (PMID: 16384981) Haines J.L. … Pericak-Vance M.A. (Invest. Ophthalmol. Vis. Sci. 2006) 3 22 46 64
  4. Association of polymorphisms in CYP17A1, MTP, and VLDLR with bone mineral density in community-dwelling Japanese women and men. (PMID: 15953542) Yamada Y. … Shimokata H. (Genomics 2005) 3 22 46 64
  5. A cellular receptor of human rhinovirus type 2, the very-low-density lipoprotein receptor, binds to two neighboring proteins of the viral capsid. (PMID: 12857919) Neumann E. … Hewat E.A. (J. Virol. 2003) 3 4 22 64

Products for VLDLR Gene

Sources for VLDLR Gene

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